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3g3l

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of putative membrane-associated protein of unknown function (YP_211325.1) from Bacteroides fragilis NCTC 9343 at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 3g3l Target Id 393243
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS24861,YP_211325.1, 332464 Molecular Weight 34517.78 Da.
    Residues 326 Isoelectric Point 4.71
    Sequence aevdqatkpaeakyyiagtitdattgqelttakvtlgdksvtssfneqvnykaegyalvvsadgyypvk rqvylnqvsdgqtsvatvnvalvsveaavippvvpptdpetdinegeatkvadkavevakpsestvtdm lagttatpeekkaldetlemaggmkvgettpevladgsilaitpvkftnpiqdapamvpyfynegcelt gdvkevaapvtradgavaadiqkaflsnaakalnmnagfvqkigytrisvlngysilgytikgqlvskk ltflisgkyyegivsyqksvmiypnyyshdshdshdshgfnpnagggsnd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.20 Rfree 0.206
    Matthews' coefficent 4.28 Rfactor 0.170
    Waters 210 Solvent Content 71.25

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    YP_211325.1 is annotated as a hypothetical protein. The protein can not be assigned to any PFAM family either on the basis of its sequence.

    The protein structure consists of beta-sheet mostly and two distinct domains can be seen in the structure: a small beta-barrel domain on the top and a larger strand+helix domain.

    GS13738B.pngGS13738B_domains.png

            Secondary structures                                                      N-terminal domain (green) and C-terminal domain (cyan)

    The structure seems to be unique; a search for structural homologs through SSM and DALI servers does not return any significant hits.

     

    Another search for structural homologs based on the two indidual domains of the protein return some hits.
    N-terminal domain (residues 41-128):
    DALI Results:

    N

    PDB

    Z-score

    RMSD

    LALI

    NRES

    %id

    Title

    1

    1h8l

    9.9

    3.1

    79

    380

    27

    Carboxypeptidase Gp180 Residues 503-882

    2

    1qmu

    9.8

    3.2

    79

    380

    27

    Carboxypeptidase Gp180 Residues 503-882

    3

    2nsm

    9.3

    3.3

    78

    390

    22

    Carboxypeptidase N Catalytic Chain

    4

    1ti2

    7.9

    2.1

    70

    274

    21

    Pyrogallol Hydroxytransferase Large Subunit

    5

    3e8v

    7.8

    2.2

    69

    82

    16

    Possible Transglutaminase-Family Protein

    6

    1uwy

    7.4

    3.2

    79

    393

    16

    Carboxypeptidase M

    7

    1dmh

    7.3

    2.6

    83

    309

    23

    Catechol 1,2-Dioxygenase

    8

    2boy

    7.0

    2.5

    82

    253

    16

    3-Chlorocatechol 1,2-Dioxygenase

    9

    1s9a

    7.0

    2.2

    82

    256

    21

    Chlorocatechol 1,2-Dioxygenase

    10

    1dlq

    6.4

    2.6

    83

    309

    23

    Catechol 1,2-Dioxygenase


    SSM Results:

    N

    PDB

    Q-score

    RMSD

    Title

    1

    3e8v

    0.4334

    2.076

    Possible Transglutaminase-Family Protein

    2

    2h0f

    0.3809

    2.118

    Pucm In The Presence Of 8-Azaxanthine

    3

    2j71

    0.3132

    2.498

    Family 41 Carbohydrate Binding Module

    4

    3fcg

    0.3015

    2.597

    Middle Domain Of The Caf1a Usher



    C-terminal domain (residues 129-336):
    DALI Results:

    N

    PDB

    Z-score

    RMSD

    LALI

    NRES

    %id

    Title

    1

    1w3g

    5.5

    4.8

    122

    312

    5

    Hemolytic Lectin From Laetiporus Sulphureus

    2

    1w3f

    5.5

    4.9

    122

    312

    5

    Hemolytic Lectin From Laetiporus Sulphureus

    3

    1w3a

    5.4

    4.7

    121

    312

    6

    Hemolytic Lectin Lsla

    4

    1uyj

    4.5

    4.2

    114

    273

    6

    Epsilon-Toxin

    5

    1jn5

    4.4

    5.0

    96

    136

    10

    P15

     

    SSM     Results:

    N

    PDB

    Q-score

    RMSD

    Title

    1

    1zpl

    0.06203

    3.962

    F17a-G Lectin Domain

    2

    2o6p

    0.06192

    5.890

    Heme-Isdc Complex

     

    An examination of the above structures compared with this target indicates that 2boy (cyan) and 3e8v (magenta) are closest match to the N-terminal domain of this target (green) (see below). This suggests a possible role of transglutaminase/dioxygenase for the N-terminal domain.

    N-term_2boy_3e8v.png

     Although the top DALI hit, 1h8l, has the best match for 79 residues, this represents a small domain of this protein (see below) and thus may not represent the same function. Moreover, the Zn ion and the bound inhibitor, GEM, are located in the active site on the other side of the protein.

     

     N-term_1h8l_new.png

    N-terminal domain (green) superimposed on 1h8l (magenta)

    Similarly, the closest match for the C-terminal domain is 1w3f, a hemolytic lectin protein. A superposition is shown below (target green, 1wef magenta).  Judging by the differences in size of these structures as well as presence of helices in this target, it may not be reasonable to assign 1wef's function to this target.

    c_term_1w3f.png 

    Ligand Summary

    Reviews

    References

     

    No references found.

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